JAL-2714 HMMSearch cutoff by E-Value, Score or None

[jalview.git] / src / jalview / hmmer / HMMSearch.java

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index 7738cb5..efc34ae 100644 (file)
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -31,10 +31,39 @@ import javax.swing.JOptionPane;
 
 public class HMMSearch extends HmmerCommand
 {
-  private static final String PARAMNAME_NO_OF_RESULTS = MessageManager.getString("label.number_of_results");
-
   static final String HMMSEARCH = "hmmsearch";
 
+  /*
+   * constants for i18n lookup of passed parameter names
+   */
+  static final String DATABASE_KEY = "label.database";
+
+  static final String THIS_ALIGNMENT_KEY = "label.this_alignment";
+
+  static final String USE_ACCESSIONS_KEY = "label.use_accessions";
+
+  static final String AUTO_ALIGN_SEQS_KEY = "label.auto_align_seqs";
+
+  static final String NUMBER_OF_RESULTS_KEY = "label.number_of_results";
+
+  static final String TRIM_TERMINI_KEY = "label.trim_termini";
+
+  static final String REPORTING_CUTOFF_KEY = "label.reporting_cutoff";
+
+  static final String CUTOFF_NONE = "None";
+
+  static final String CUTOFF_SCORE = "Score";
+
+  static final String CUTOFF_EVALUE = "E-Value";
+
+  static final String SEQ_EVALUE_KEY = "label.seq_evalue";
+
+  static final String DOM_EVALUE_KEY = "label.dom_evalue";
+
+  static final String SEQ_SCORE_KEY = "label.seq_score";
+
+  static final String DOM_SCORE_KEY = "label.dom_score";
+
   boolean realign = false;
 
   boolean trim = false;
@@ -130,65 +159,80 @@ public class HMMSearch extends HmmerCommand
     List<String> args = new ArrayList<>();
     args.add(command);
     args.add("-o");
-    args.add(searchOutputFile.getAbsolutePath());
+    args.add(getFilePath(searchOutputFile));
     args.add("-A");
-    args.add(hitsAlignmentFile.getAbsolutePath());
+    args.add(getFilePath(hitsAlignmentFile));
 
     boolean dbFound = false;
     String dbPath = "";
     File databaseFile = null;
 
+    boolean useEvalueCutoff = false;
+    boolean useScoreCutoff = false;
+    String seqEvalueCutoff = null;
+    String domEvalueCutoff = null;
+    String seqScoreCutoff = null;
+    String domScoreCutoff = null;
+
     if (params != null)
     {
       for (ArgumentI arg : params)
       {
         String name = arg.getName();
-        if (MessageManager.getString("label.number_of_results")
+        if (MessageManager.getString(NUMBER_OF_RESULTS_KEY)
                 .equals(name))
         {
           seqsToReturn = Integer.parseInt(arg.getValue());
         }
-        else if (MessageManager.getString("label.auto_align_seqs")
+        else if (MessageManager.getString(AUTO_ALIGN_SEQS_KEY)
                 .equals(name))
         {
           realign = true; // TODO: not used
         }
-        else if (MessageManager.getString("label.use_accessions")
+        else if (MessageManager.getString(USE_ACCESSIONS_KEY)
                 .equals(name))
         {
           args.add("--acc");
         }
-        else if (MessageManager.getString("label.seq_e_value").equals(name))
+        else if (MessageManager.getString(REPORTING_CUTOFF_KEY)
+                .equals(name))
+        {
+          if (CUTOFF_EVALUE.equals(arg.getValue()))
+          {
+            useEvalueCutoff = true;
+          }
+          else if (CUTOFF_SCORE.equals(arg.getValue()))
+          {
+            useScoreCutoff = true;
+          }
+        }
+        else if (MessageManager.getString(SEQ_EVALUE_KEY).equals(name))
         {
-          args.add("--incE");
-          args.add(arg.getValue());
+          seqEvalueCutoff = arg.getValue();
         }
-        else if (MessageManager.getString("label.seq_score").equals(name))
+        else if (MessageManager.getString(SEQ_SCORE_KEY).equals(name))
         {
-          args.add("-incT");
-          args.add(arg.getValue());
+          seqScoreCutoff = arg.getValue();
         }
-        else if (MessageManager.getString("label.dom_e_value_desc")
+        else if (MessageManager.getString(DOM_EVALUE_KEY)
                 .equals(name))
         {
-          args.add("--incdomE");
-          args.add(arg.getValue());
+          domEvalueCutoff = arg.getValue();
         }
-        else if (MessageManager.getString("label.dom_score").equals(name))
+        else if (MessageManager.getString(DOM_SCORE_KEY).equals(name))
         {
-          args.add("--incdomT");
-          args.add(arg.getValue());
+          domScoreCutoff = arg.getValue();
         }
-        else if (MessageManager.getString("label.trim_termini")
+        else if (MessageManager.getString(TRIM_TERMINI_KEY)
                 .equals(name))
         {
           trim = true;
         }
-        else if (MessageManager.getString("label.database").equals(name))
+        else if (MessageManager.getString(DATABASE_KEY).equals(name))
         {
           dbFound = true;
           dbPath = arg.getValue();
-          if (!MessageManager.getString("label.this_alignment")
+          if (!MessageManager.getString(THIS_ALIGNMENT_KEY)
                   .equals(dbPath))
           {
             databaseFile = new File(dbPath);
@@ -197,7 +241,22 @@ public class HMMSearch extends HmmerCommand
       }
     }
 
-    if (!dbFound || MessageManager.getString("label.this_alignment")
+    if (useEvalueCutoff)
+    {
+      args.add("-E");
+      args.add(seqEvalueCutoff);
+      args.add("--domE");
+      args.add(domEvalueCutoff);
+    }
+    else if (useScoreCutoff)
+    {
+      args.add("-T");
+      args.add(seqScoreCutoff);
+      args.add("--domT");
+      args.add(domScoreCutoff);
+    }
+
+    if (!dbFound || MessageManager.getString(THIS_ALIGNMENT_KEY)
             .equals(dbPath))
     {
       /*
@@ -214,16 +273,10 @@ public class HMMSearch extends HmmerCommand
         copy.deleteSequence(hmmSeq);
       }
       exportStockholm(copy.getSequencesArray(), databaseFile, null);
-      // StockholmFile stoFile = new StockholmFile(copy);
-      // stoFile.setSeqs(copy.getSequencesArray());
-      // String alignmentString = stoFile.print();
-      // PrintWriter writer = new PrintWriter(databaseFile);
-      // writer.print(alignmentString);
-      // writer.close();
     }
 
-    args.add(hmmFile.getAbsolutePath());
-    args.add(databaseFile.getAbsolutePath());
+    args.add(getFilePath(hmmFile));
+    args.add(getFilePath(databaseFile));
 
     return runCommand(args);
   }
@@ -273,7 +326,7 @@ public class HMMSearch extends HmmerCommand
       if (trim)
       {
         alignArgs.add(new BooleanOption(
-                MessageManager.getString("label.trim_termini"),
+                MessageManager.getString(TRIM_TERMINI_KEY),
                 MessageManager.getString("label.trim_termini_desc"), true,
                 true, true, null));
       }